IBD-microbiome-meta

These scripts and intermediary files have been created used to perform the analyses in our study "Temporal strain-resolved metagenomics associates IBD dysbiosis with gastrointestinal inflammation" authored by Rebecca Ansorge, Stefano Romano, Clémence Frioux, Tamás Korcsmáros, Myeonghyun Yoou, Nathalie Juge, Katarzyna Sidorczuk, Falk Hildebrand

The code was tailored to our study to allow more detailed understanding of the analyses and allow better reproducibility and do not represent tools and scripts for general use.

List of R scripts used for analyses

Misc

Resampling: Resampling_submit.Rmd
Prevalence filtration: Prevalence_filtration_q0.1_submit.Rmd, Pevalence_functions.r
Combine results into overview table:Combine_MGSresults_tables_q0.1_submit.Rmd \

Beta-diversity

Beta-diversity overall: Beta_IBD_submit.Rmd
Longitudinal analyses beta-diversity and inflammation index: Temporal_variation_Beta_submit.Rmd
Make beta-diversity figure and statistics: MakeFig_Beta_submit.Rmd \

Differential abundance

Make differential abundance figure and statistics: MakeFig_DA_0.1_submit.Rmd
Differential abundance meta-analyses IBD subtypes and controls: DA_meta_IBD_UCvsCD_submit.Rmd, DA_function_UCvsCD.R
Differential abundance meta-analyses IBD and controls: DA_meta_IBD_submit.Rmd, DA_function.R \

Inflamation index

Compare inflammation index and differential abundances: humanRds_vs_DAq0.1_submit.Rmd \

Strains

Make Strain figure 3: MakeFig_Strains_q0.1_submit.Rmd
Analyse strain permanova results and compare with differential abundances: strain_pmva_R2vsDA_lm_Jun23_DAq0.1_submit.Rmd
Strains figure 4: IBD_strains_functions.R, _targets.R \

Enterosignatures

Make enterosignature figure and statistics: MakeFig_ES_submit.Rmd
Phyla abundances: MakeFIg_PhylaAb_hr_submit.Rmd \

Data

Generally all required inputs and intermediary files are provided needed to run the scripts.
DAmeans.ALL.0.1.txt : Differential abundance analysis results all comparisons
DAmeans.CDHC.0.1.txt : Differential abundance analysis results CD vs control
DAmeans.CDUC.0.1.txt : Differential abundance analysis results CD vs UC
DAmeans.IBDHC.0.1.txt : Differential abundance analysis results IBD vs control
DAmeans.UCHC.0.1.txt : Differential abundance analysis results UC vs control
DA.num.overview.0.1.txt : Numbers of MGS differentially abundant
IBDmeta.cur.filt.mc.matched.1TimeP.txt : Metadata first timepoint
IBDmeta.cur.filt.mc.matched.txt : Metadata first timepoint
IBDmeta.cur.filt.mc.overview.txt : Metadata summary
IBD.MGSabundance.txt : MGS abundances
IBD.MGStaxa.txt : MGS taxonomy
IQtree_allsites.treefile : MGS tree
MetagStats.csv : Stats from MATAFILER run
MGScorvsDAibd.q0.1.crosslong.csv : Correlation between DA effect and inflammation index
MGS.matL0.txt : Kingdom-aggegated abundances
MGS.matL1.txt : Phylum-aggegated abundances
MGS.matL2.txt : Class-aggegated abundances
MGS.matL3.txt : Order-aggegated abundances
MGS.matL4.txt : Family-aggegated abundances
MGS.matL5.txt : Genus-aggegated abundances
MGS.matL6.txt : Species-aggegated abundances
phylum_hr_correlation.txt : Correlation between phylum abundances and inflammation index
prev.filt.MGS.txt : prevelence filtered MGS
resampling.20.txt : Samples from resampling procedure IBD, controls
resampling.CDUC.20.txt : Samples from resampling procedure IBD subtypes, controls
resampling.png : Resampling procedure
DA_analysis/beta.dbrda.data.rds : dbRDA results
DA_analysis/beta.df_all_cross.rds : Beta-diversity cross-sectional results dataframe
DA_analysis/beta.l_spec.long.distances.df.20ibd2.rds : Temporal variance beta-diversity longitudinal data IBD, controls
DA_analysis/beta.l_spec.long.distances.df.20.rds : Temporal variance beta-diversity longitudinal data IBD subtypes, controls
DA_analysis/beta.pair.tempInd.rds : Average beta-diversity among 4 consecutive samples per Individual
DA_analysis/beta.pcoa.data.rds : PcoA results
DA_analysis/beta.pmva.bc.cohort.rds : Permanova results cohort effect
DA_analysis/beta.pmva.bc.ibd.rds : Permanova results IBD, controls
DA_analysis/beta.pmvaPair.bc.ibd2.rds : Permanova results IBD subtypes, controls
DA_analysis/dist_hr_indNest_log2_lm_perCohort.rds : Nested (individuls nexted in cohort) linear model on intra-individual microbiome dissimilarity associated to inflammation index
DA_analysis/l.meta_cdcontrols.rds : Meta-analysis differential abundance CD vs controls
DA_analysis/l.meta.cdhc.prevfilt.rds : Prevalence-filtered meta-analysis differential abundance CD vs controls
DA_analysis/l.meta.cdhc.prevfilt.sign0.1.20.rds : Robust significant (q<0.1) species differentially abundant in all 20 resamplings, CD vs controls
DA_analysis/l.meta.cdhc.prevfilt.sign0.1.rds : Significant (q<0.1) species differentially abundant in 1-20 resamplings, CD vs controls
DA_analysis/l.meta.cduc.prevfilt.rds : Prevalence-filtered meta-analysis differential abundance CD vs UC
DA_analysis/l.meta.cduc.prevfilt.sign0.1.20.rds : Robust significant (q<0.1) species differentially abundant in all 20 resamplings, CD vs UC
DA_analysis/l.meta.cduc.prevfilt.sign0.1.rds : Significant (q<0.1) species differentially abundant in 1-20 resamplings, CD vs UC
DA_analysis/l.meta.prevfilt.rds : Prevalence-filtered meta-analysis differential abundance IBD vs controls
DA_analysis/l.meta.prevfilt.sign0.1.20.rds : Robust significant (q<0.1) species differentially abundant in all 20 resamplings, IBD vs controls
DA_analysis/l.meta.prevfilt.sign0.1.rds : Significant (q<0.1) species differentially abundant in 1-20 resamplings, IBD vs controls
DA_analysis/l.meta.rds : Meta-analysis differential abundance IBD vs controls
DA_analysis/l.meta_uccd.rds : Meta-analysis differential abundance UC vs CD
DA_analysis/l.meta_uccontrols.rds : Meta-analysis differential abundance UC vs. controls
DA_analysis/l.meta.uchc.prevfilt.rds : Prevalence-filtered meta-analysis differential abundance UC vs controls
DA_analysis/l.meta.uchc.prevfilt.sign0.1.20.rds : Robust significant (q<0.1) species differentially abundant in all 20 resamplings, UC vs controls
DA_analysis/l.meta.uchc.prevfilt.sign0.1.rds : Significant (q<0.1) species differentially abundant in 1-20 resamplings, UC vs controls
DA_analysis/perInd_dist_vs_deltaHR.rds : Per-indifidual Bray-Curtis dissimilarity vs change in inflammation index
ES/h_scaled.tsv : Enterosignature abundance weights
ES/model_fit.tsv : Enterosignature model fit scores
ES/reapply_NMF_IBD.ipynb : Enterosignature analysis
humanReads/dist.HL_hr_cond_gat_intrChrt.rds : High and low inflammation index groups per cohort
humanReads/dist.HL_hr_ind_gat_intraInd.rds : High and low inflammation index groups within individuals
humanReads/humRds_cor_MGS_list_CTRL.rds : Correlation between DA effect and inflammation index control only
humanReads/humRds_cor_MGS_list_IBD.rds : Correlation between DA effect and inflammation index IBD only
humanReads/humRds_cor_MGS_list.rds : Correlation between DA effect and inflammation index
humanReads/MGScor_blInd_DA_gat.q0.1.rds : Significant correlation between DA effect and inflammation index blocked in individuals
humanReads/MGScorvsDAibd.crosslong.CTRLonly.q0.1.rds : Significant correlation between DA effect and inflammation index control only \ humanReads/MGScorvsDAibd.crosslong.IBDonly.q0.1.rds : Significant correlation between DA effect and inflammation index IBD only
humanReads/MGScorvsDAibd.crosslong.q0.1.rds : Significant correlation between DA effect and inflammation index
rds/cohort_summary.rds : Cohort summary
rds/meta_hr.rds : Metadata with human read percent
rds/MGS.toptax_DAFigq0.1.rds : Top taxa shown in Figure 2
rds/overview.MGS.DA_q0.1_strains_cor_genes_PosNegSeparate.rds : Overview Data of various analyses combined
strains/ibd2.strains.pmva.all.June23.rds : Permanova results un cophenetic distances of strains IBD, controls
strains/ibd.strains.pmva.all.June23.rds : Permanova results un cophenetic distances of strains IBD subtypes, controls
strains/StrainClust.overlapIBD_IBD2.June23.rds : Overlap of robust strain clusters IBD/controls vs CD/UC/controls
strains/StrainClust.overlapIBD_IBD2.variable.June23.rds : Overlap of variable strain clusters IBD/controls vs CD/UC/controls
strains/strainR2vsDA.lm.June23_q0.1.rds : Linear model comparing strain clusterind and species differential abundances
strains/strainR2vsTE.inclNonSig.ibd_ibd2.June23.rds : Results from linear model comparing strain clusterind and species differential abundances IBD subtypes, controls
strains/strainR2vsTE.inclNonSig_q0.1.June23.rds : Results from linear model comparing strain clusterind and species differential abundances IBD, controls
strains/strainR2vsTE.incTips_q0.1.June23.rds : Results from linear model comparing strain clusterind and species differential abundances IBD, controls (only significant)
strains/tree.df.prev.June23.rds : Number of tips per MGS-tree